Hi - This is only rough but something like the below should work on your data:
This makes the assumption that:
There is only 1 file in the 'annovar' directory which has the same prefix (delimited by an underscore) as the associated file in the 'files' directory and it exists
This is not just applicable for '123_' but for all files
I have an if statement where I state that if there are more than one records (lines) found containing a string in a file, then it enters into a while loop to use each line for as many lines as there are and then stop.
Trouble is, I can't figure out how to move to the next instance of each line. ... (2 Replies)
Below is a test script to illustrate a problem from a larger script I am writing.
$ cat /tmp/loggingtest
#!/bin/bash
lvcreate -s -l 100%FREE -n var-data-snapshot vg00/var-data 2> >(logger -t "loggingtest.crit") 1> >(logger -t "loggingtest.info")
sync &
wait
lvremove -f... (1 Reply)
I have a file with hundreds of records and I need to find those records that have three digits at the beginning and the same three digits at the end.
$GREP '\(\)\(\)\(\)\3\2\1'I
believe this is part of the script but I am not sure how to compare these 3 digits with the 3 digits at the end of... (2 Replies)
Hi there, im sure this is really simple but i have some strings like this
e1000g123001
e1000g0
nge11101
nge3and i want to create two variables ($DRIVER and $INSTANCE). the first one containing the alpha characters that make up the first part of the string, e.g. e1000g or nge and the... (9 Replies)
hi,
i've bash script thats working...
but now i need to add a line....that prompts for user input....like yes and 1 as complete install....
so here's how it looks...
$ cd 9200 (cd into directory)
$./install (hv to type ./install to run install then ask for)
----do you want to... (4 Replies)
two files: one with the line number only, and the 2nd one with line number and content, as following:
line_file.txt
1
3
5
9
23
30
content_file.txt
1|we are the world|good|great
2|easily do this by highlighting you|easily do this by highlighting you|easily do this by highlighting... (2 Replies)
Hi I have a problem, I am attempting to write a bash script that goes through a file and can determine how many characters are at a set point in a line starting with QTY+113:100:PCE, If it detects 3 digits (number in bold) then pad it out with 12 zero's
If there are only two digits then pad it... (8 Replies)
In the bash below the user selects the file to be used. The digits of each file are unique and used to automatically locate the next file to be used in the process. The problem I can not seem to fix is that the full path needs to be referenced in the second portion and it is not currently. Is... (7 Replies)
In the bash below I am asking the user for a panel and reading that into bed. Then asking the user for a file and reading that into file1.Is the grep in bold the correct way to apply the selected panel to the file? I am getting a syntax error. Thank you :)
... (4 Replies)
As part of a bash the below line strips off a numerical prefix from directory 1 to search for in directory 2.
for file in /home/cmccabe/Desktop/comparison/missing/*.txt
do
file1=${file##*/} # Strip off directory
getprefix=${file1%%_*.txt}
... (5 Replies)
Discussion started by: cmccabe
5 Replies
LEARN ABOUT CENTOS
bashbug
BASHBUG(1) General Commands Manual BASHBUG(1)NAME
bashbug - report a bug in bash
SYNOPSIS
bashbug [--version] [--help] [email-address]
DESCRIPTION
bashbug is a shell script to help the user compose and mail bug reports concerning bash in a standard format. bashbug invokes the editor
specified by the environment variable EDITOR on a temporary copy of the bug report format outline. The user must fill in the appropriate
fields and exit the editor. bashbug then mails the completed report to bug-bash@gnu.org, or email-address. If the report cannot be
mailed, it is saved in the file dead.bashbug in the invoking user's home directory.
The bug report format outline consists of several sections. The first section provides information about the machine, operating system,
the bash version, and the compilation environment. The second section should be filled in with a description of the bug. The third sec-
tion should be a description of how to reproduce the bug. The optional fourth section is for a proposed fix. Fixes are encouraged.
ENVIRONMENT
bashbug will utilize the following environment variables if they exist:
EDITOR Specifies the preferred editor. If EDITOR is not set, bashbug defaults to emacs.
HOME Directory in which the failed bug report is saved if the mail fails.
TMPDIR Directory in which to create temporary files and directories.
SEE ALSO bash(1)AUTHORS
Brian Fox, Free Software Foundation
bfox@gnu.org
Chet Ramey, Case Western Reserve University
chet@po.cwru.edu
GNU Bash-4.0 1998 July 30 BASHBUG(1)